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Sample GSM211607 Query DataSets for GSM211607
Status Public on Feb 29, 2008
Title mibta52b 72h (AH_WT72hVsta52b72h_BRII_TR1_133)
Sample type RNA
 
Channel 1
Source name mib mutant embryos
Organism Danio rerio
Characteristics mib mutant embryos
Extracted molecule total RNA
Extraction protocol Total RNA extraction using Trizol followed by Qiagen RNeasy Mini Kit extraction
Label Cy-5 d-UTP
Label protocol 20ug of total RNA was reverse transcribed to produce Cy-5 d-UTP (Sample) cDNA targets
 
Channel 2
Source name wild type embryos
Organism Danio rerio
Characteristics wild type siblings
Extracted molecule total RNA
Extraction protocol Total RNA extraction using Trizol followed by Qiagen RNeasy Mini Kit extraction
Label Cy3 d-UTP
Label protocol 20ug of total RNA was reverse transcribed to produce Cy3 d-UTP (Reference) cDNA targets
 
 
Hybridization protocol Standard procedure (Mathavan et al., 2005)
Scan protocol GenePix 4000B microarray scanner (Axon Instruments)
Description RNA from mib mutant embryos and their wild type siblings at three different time points
Data processing The intensity-based log ratio median method (Yang et al./, 2003)
 
Submission date Jul 19, 2007
Last update date Oct 26, 2007
Contact name Govindarajan Kunde Ramamoorthy
E-mail(s) mathavans@gis.a-star.edu.sg
Phone +65-64788059
Fax +65-64789058
Organization name Genome Institute of Singapore
Department Research Computing Group
Street address 60, Biopolis Street, Genome
City Singapore
ZIP/Postal code 138672
Country Singapore
 
Platform ID GPL2715
Series (1)
GSE8522 RNA from 3 d and 2 d old embryos of mibta52b, mibm132 and mibtfi91, and RNA from 3 d, 2d and 1 d old embryos of mibta52b

Data table header descriptions
ID_REF Unique ID
VALUE Normalized log2 ratio of means defined by CH1/CH2
CH1_Median CH1(F635) median fluorescence intensity
CH1_MEAN CH1 (F635) mean fluorescence intensity
CH1_SD CH1 (F635) fluorescence intensity standard deviation
CH1_BKD_Median CH1 (F635) background median fluorescence intensity
CH1_BKD_MEAN CH1 (F635) background mean fluorescence intensity
CH1_BKD_SD CH1 (F635) background fluorescence intensity standard deviation
%>CH1_BKD_+2SD % of feature pixels greater than two standard deviations over the background
CH2_Median CH2(F532) median fluorescence intensity
CH2_MEAN CH2 (F532) mean fluorescence intensity
CH2_SD CH2 (F532) fluorescence intensity standard deviation
CH2_BKD_Median CH2 (F532) background median fluorescence intensity
CH2_BKD_MEAN CH2 (F532) background mean fluorescence intensity
CH2_BKD_SD CH2 (F532) background fluorescence intensity standard deviation
%>CH2_BKD_+2SD % of feature pixels greater than two standard deviations over the background
Ratio_of_Means Unnormalized ratio of means defined by CH1/CH2
AREA Number of feature pixels
BKD_AREA Number of feature background pixels
CH1_Median-CH1_BKD Channel 1 median signal
CH2_Median-CH2_BKD Channel 2 median signal
CH1_Mean-CH1_BKD Channel 1 mean signal
CH2_Mean-CH2_BKD Channel 2 mean signal

Data table
ID_REF VALUE CH1_Median CH1_MEAN CH1_SD CH1_BKD_Median CH1_BKD_MEAN CH1_BKD_SD %>CH1_BKD_+2SD CH2_Median CH2_MEAN CH2_SD CH2_BKD_Median CH2_BKD_MEAN CH2_BKD_SD %>CH2_BKD_+2SD Ratio_of_Means AREA BKD_AREA CH1_Median-CH1_BKD CH2_Median-CH2_BKD CH1_Mean-CH1_BKD CH2_Mean-CH2_BKD
5269516 1.9708 32495 32549 4962 99 107 68 100 19551 18512 3670 94 99 91 100 1.762 120 717 32396 19457 32442 18413
5269517 1.7711 38884 35916 11050 90 125 499 98 25063 22717 7149 90 95 48 98 1.583 156 944 38794 24973 35791 22622
5269518 0.6809 518 518 146 87 91 39 98 825 812 208 104 107 31 97 .609 156 920 431 721 427 705
5269519 3.8338 25142 24636 3180 99 105 51 100 7759 7274 1820 115 118 33 100 3.427 120 748 25043 7644 24531 7156
5269520 1.5058 660 644 167 84 89 40 99 528 512 156 96 98 23 94 1.346 120 704 576 432 555 414
5269521 0.9853 246 253 90 83 87 41 82 277 282 65 89 93 32 98 .881 120 794 163 188 166 189
5269522 1.1466 755 778 232 83 97 77 99 772 765 197 87 98 56 95 1.025 120 743 672 685 681 667
5269523 1.1931 369 364 140 76 81 35 92 359 357 125 87 90 35 93 1.067 120 745 293 272 283 267
5269524 1.0182 760 786 178 86 161 303 66 842 862 139 93 147 198 100 .91 80 615 674 749 625 715
5269525 0.8625 544 555 138 80 94 77 100 710 707 152 91 109 95 98 .771 120 808 464 619 461 598
5269526 1.0600 655 645 151 84 90 47 100 670 689 161 97 102 43 100 .948 120 806 571 573 555 587
5269527 0.7495 397 417 139 84 92 64 94 582 595 171 98 106 59 100 .67 120 850 313 484 325 489
5269528 1.2506 1410 1398 432 91 102 74 98 1212 1262 326 93 98 33 100 1.118 120 784 1319 1119 1296 1164
5269529 1.5333 1104 1049 355 84 123 524 42 819 792 240 88 92 34 94 1.371 156 856 1020 731 926 700
5269530 1.1112 1312 1288 306 89 95 42 98 1336 1314 303 107 114 44 98 .993 156 838 1223 1229 1193 1200
5269531 1.7878 2141 2115 351 90 96 42 100 1474 1383 368 116 120 29 96 1.598 120 741 2051 1358 2019 1263
5269532 1.0478 224 234 90 86 104 278 0 257 256 75 98 203 1973 0 .937 120 666 138 159 130 53
5269533 1.1498 291 304 99 83 97 124 34 294 304 71 89 106 132 22 1.028 120 738 208 205 207 198
5269534 1.7714 468 470 135 82 98 79 94 337 336 89 91 102 52 95 1.584 120 678 386 246 372 234
5269535 0.1329 210 220 95 77 81 37 78 1285 1294 156 90 93 38 100 .119 80 630 133 1195 139 1201

Total number of rows: 16512

Table truncated, full table size 1517 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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